[2024-01-24 13:12:53,912] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:53,915] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:53,915] [INFO] DQC Reference Directory: /var/lib/cwl/stg309db8f7-ac52-4c01-8117-cbaa9c014da0/dqc_reference
[2024-01-24 13:12:55,289] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:55,295] [INFO] Task started: Prodigal
[2024-01-24 13:12:55,295] [INFO] Running command: gunzip -c /var/lib/cwl/stgba3e6404-0f5a-456b-9c27-865bb5b7b48a/GCF_027947535.2_ASM2794753v2_genomic.fna.gz | prodigal -d GCF_027947535.2_ASM2794753v2_genomic.fna/cds.fna -a GCF_027947535.2_ASM2794753v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:29,484] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:29,484] [INFO] Task started: HMMsearch
[2024-01-24 13:13:29,484] [INFO] Running command: hmmsearch --tblout GCF_027947535.2_ASM2794753v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg309db8f7-ac52-4c01-8117-cbaa9c014da0/dqc_reference/reference_markers.hmm GCF_027947535.2_ASM2794753v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:29,864] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:29,865] [INFO] Found 6/6 markers.
[2024-01-24 13:13:29,928] [INFO] Query marker FASTA was written to GCF_027947535.2_ASM2794753v2_genomic.fna/markers.fasta
[2024-01-24 13:13:29,929] [INFO] Task started: Blastn
[2024-01-24 13:13:29,929] [INFO] Running command: blastn -query GCF_027947535.2_ASM2794753v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg309db8f7-ac52-4c01-8117-cbaa9c014da0/dqc_reference/reference_markers.fasta -out GCF_027947535.2_ASM2794753v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:31,375] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:31,379] [INFO] Selected 24 target genomes.
[2024-01-24 13:13:31,379] [INFO] Target genome list was writen to GCF_027947535.2_ASM2794753v2_genomic.fna/target_genomes.txt
[2024-01-24 13:13:31,401] [INFO] Task started: fastANI
[2024-01-24 13:13:31,401] [INFO] Running command: fastANI --query /var/lib/cwl/stgba3e6404-0f5a-456b-9c27-865bb5b7b48a/GCF_027947535.2_ASM2794753v2_genomic.fna.gz --refList GCF_027947535.2_ASM2794753v2_genomic.fna/target_genomes.txt --output GCF_027947535.2_ASM2794753v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:14,397] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:14,397] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg309db8f7-ac52-4c01-8117-cbaa9c014da0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:14,398] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg309db8f7-ac52-4c01-8117-cbaa9c014da0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:14,418] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:14:14,418] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:14:14,418] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	82.6603	1358	2830	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	81.3631	1201	2830	95	below_threshold
Streptomyces pathocidini	strain=NRRL B-24287	GCA_001418495.1	1650571	1650571	type	True	80.4721	786	2830	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	80.3603	971	2830	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	80.2997	1015	2830	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	80.2878	1048	2830	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	80.2832	926	2830	95	below_threshold
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	80.1765	1284	2830	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	80.1126	1229	2830	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	80.0055	1150	2830	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	79.9952	1032	2830	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	79.9348	1052	2830	95	below_threshold
Streptomyces morookaense	strain=DSM 40503	GCA_013030945.1	1970	1970	type	True	79.9337	1031	2830	95	below_threshold
Streptomyces morookaense	strain=JCM 4793	GCA_014656115.1	1970	1970	type	True	79.9041	1061	2830	95	below_threshold
Streptomyces piniterrae	strain=jys28	GCA_005048155.1	2571125	2571125	type	True	79.8462	1100	2830	95	below_threshold
Streptomyces sparsogenes	strain=ATCC 25498	GCA_001704635.1	67365	67365	type	True	79.8262	1174	2830	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	79.8112	921	2830	95	below_threshold
Streptomyces sparsogenes	strain=DSM 40356	GCA_001969965.1	67365	67365	type	True	79.7845	1112	2830	95	below_threshold
Streptomyces caniferus	strain=NBRC 15389	GCA_009811555.1	285557	285557	type	True	79.7449	1185	2830	95	below_threshold
Streptomyces physcomitrii	strain=LD120	GCA_012273655.1	2724184	2724184	type	True	79.6852	1154	2830	95	below_threshold
Actinacidiphila oryziradicis	strain=NEAU-C40	GCA_005047355.1	2571141	2571141	type	True	79.5828	1147	2830	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	79.5735	1052	2830	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	79.5616	1132	2830	95	below_threshold
Streptomyces yatensis	strain=DSM 41771	GCA_018069625.1	155177	155177	type	True	79.4365	1261	2830	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:14,420] [INFO] DFAST Taxonomy check result was written to GCF_027947535.2_ASM2794753v2_genomic.fna/tc_result.tsv
[2024-01-24 13:14:14,420] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:14,420] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:14,421] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg309db8f7-ac52-4c01-8117-cbaa9c014da0/dqc_reference/checkm_data
[2024-01-24 13:14:14,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:14,500] [INFO] Task started: CheckM
[2024-01-24 13:14:14,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027947535.2_ASM2794753v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027947535.2_ASM2794753v2_genomic.fna/checkm_input GCF_027947535.2_ASM2794753v2_genomic.fna/checkm_result
[2024-01-24 13:16:19,248] [INFO] Task succeeded: CheckM
[2024-01-24 13:16:19,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:16:19,274] [INFO] ===== Completeness check finished =====
[2024-01-24 13:16:19,274] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:16:19,275] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027947535.2_ASM2794753v2_genomic.fna/markers.fasta)
[2024-01-24 13:16:19,275] [INFO] Task started: Blastn
[2024-01-24 13:16:19,275] [INFO] Running command: blastn -query GCF_027947535.2_ASM2794753v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg309db8f7-ac52-4c01-8117-cbaa9c014da0/dqc_reference/reference_markers_gtdb.fasta -out GCF_027947535.2_ASM2794753v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:16:21,635] [INFO] Task succeeded: Blastn
[2024-01-24 13:16:21,640] [INFO] Selected 25 target genomes.
[2024-01-24 13:16:21,640] [INFO] Target genome list was writen to GCF_027947535.2_ASM2794753v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:16:21,716] [INFO] Task started: fastANI
[2024-01-24 13:16:21,716] [INFO] Running command: fastANI --query /var/lib/cwl/stgba3e6404-0f5a-456b-9c27-865bb5b7b48a/GCF_027947535.2_ASM2794753v2_genomic.fna.gz --refList GCF_027947535.2_ASM2794753v2_genomic.fna/target_genomes_gtdb.txt --output GCF_027947535.2_ASM2794753v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:17:10,887] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:10,913] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:17:10,914] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003144095.1	s__Streptomyces sp003144095	82.8558	1313	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000240165.1	s__Streptomyces cattleya	81.559	1346	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	3	-
GCF_014203555.1	s__Streptomyces olivoverticillatus	80.3374	977	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684805.1	s__Streptomyces palmae	80.3276	1004	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083985.1	s__SCUT-3 sp014083985	80.3228	1069	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__SCUT-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091855.1	s__Streptomyces sp900091855	80.3211	1138	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_007280575.1	s__Streptomyces sp007280575	80.2901	926	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012034175.1	s__Streptomyces sp012034175	80.2009	1275	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016916835.1	s__Streptomyces bryophytorum	80.1791	1196	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_016756395.1	s__Streptomyces sp016756395	80.1295	1392	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142575.1	s__Streptomyces paucisporeus	80.1225	1226	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701325.1	s__Streptomyces sp000701325	80.0952	1188	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007595705.1	s__Streptomyces sp007595705	79.9853	1161	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013030945.1	s__Streptomyces morookaense	79.9697	1023	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013055795.1	s__Streptomyces sp013055795	79.8542	1038	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014253015.1	s__Streptomyces sp014253015	79.7536	1112	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590865.1	s__Streptomyces sp001590865	79.7527	1048	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014649355.1	s__Streptomyces althioticus	79.6968	1112	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.374	98.43	96.72	0.91	0.83	9	-
GCF_013364155.1	s__Streptomyces sp013364155	79.686	1155	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005047355.1	s__Streptomyces sp005047355	79.5525	1153	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649795.1	s__Streptomyces melanogenes	79.5277	1139	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	-
GCF_008042045.1	s__Streptomyces sp008042045	79.5219	1148	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158915.1	s__Streptomyces himastatinicus	79.4447	1260	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.59	95.41	0.86	0.82	5	-
GCF_008704425.1	s__Streptomyces fradiae	79.3627	1103	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.37	0.98	0.97	5	-
GCF_014650815.1	s__Streptomyces flavofungini	79.0347	1147	2830	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:17:10,915] [INFO] GTDB search result was written to GCF_027947535.2_ASM2794753v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:17:10,916] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:17:10,920] [INFO] DFAST_QC result json was written to GCF_027947535.2_ASM2794753v2_genomic.fna/dqc_result.json
[2024-01-24 13:17:10,921] [INFO] DFAST_QC completed!
[2024-01-24 13:17:10,921] [INFO] Total running time: 0h4m17s